Pathway Analysis for Glmnet
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
##
## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
## clusterProfiler: an R package for comparing biological themes among
## gene clusters. OMICS: A Journal of Integrative Biology 2012,
## 16(5):284-287##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:multiMiR':
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
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## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.## Loading required package: IRanges## Loading required package: S4Vectors##
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.glmnet = readRDS("data/sel_features/results_glmnet_coef.rds")
sel.features = results.glmnet
sel.features## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$mse
## (Intercept) hsa-let-7f-1 hsa-let-7f-2 hsa-mir-106b
## -4.660768998 -0.602611795 -0.303241266 0.057087793
## hsa-mir-124-1 hsa-mir-124-3 hsa-mir-125a hsa-mir-1270-1
## 0.020177143 0.198244494 -0.833181786 0.196646007
## hsa-mir-1274b hsa-mir-1277 hsa-mir-129-1 hsa-mir-129-2
## 0.049593471 -0.078061541 0.015403639 0.280394056
## hsa-mir-1296 hsa-mir-1307 hsa-mir-130b hsa-mir-135b
## 0.727554050 1.321130210 0.651952177 0.214940662
## hsa-mir-197 hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b
## 0.401597172 0.723256287 0.960442627 0.999110048
## hsa-mir-219-1 hsa-mir-2277 hsa-mir-3190 hsa-mir-3199-1
## -0.142070555 -1.028790435 -0.069032247 -0.477348224
## hsa-mir-320c-2 hsa-mir-326 hsa-mir-34a hsa-mir-3647
## -0.147939981 0.142961419 -0.490859074 -1.274187184
## hsa-mir-372 hsa-mir-3909 hsa-mir-3926-1 hsa-mir-3926-2
## 0.555923562 -0.249291482 -0.700901157 -0.193491544
## hsa-mir-3934 hsa-mir-425 hsa-mir-466 hsa-mir-513a-2
## -0.126443055 0.663266269 -0.060597443 -0.091734263
## hsa-mir-513b hsa-mir-590 hsa-mir-592 hsa-mir-605
## -0.020343279 1.765652282 -0.340787399 -0.602116044
## hsa-mir-624 hsa-mir-625 hsa-mir-659 hsa-mir-664
## -0.006093003 -0.280042060 -1.147481063 -0.659063456
## hsa-mir-7-1 hsa-mir-935 MRE11A.R2Gn ASNS.R2Gn
## 2.240551045 0.026797327 3.652583446 0.006499477
## AKT1.R2Gn CDKN1A.R2Gn PEA15.R2Gn MAPK1.R2Gn
## -1.224207246 -0.029941119 0.345050564 0.152560731
## STK11.R2Gn ADAR.R2Gn MAPK3.R2Gn ACVRL1.R2Gn
## -0.413942070 0.181242058 -1.455678002 1.328790395
## TSC2.R2Gn YBX1.R2Gn JUN.R2Gn CHEK1.R2Gn
## -0.090962103 0.379066706 -0.040587687 1.769312869
## ACACA.R2Gn RAB11B.R2Gn EEF2K.R2Gn BCL2L1.R2Gn
## 0.307049276 -0.680852733 -0.941267013 -0.358595133
## MSH6.R2Gn DVL3.R2Gn PRKAA1.R2Gn FOXM1.R2Gn
## 0.156468978 0.098525028 -0.085103817 0.277582923
## YWHAB.R2Gn BAX.R2Gn CASP9.R2Gn CHGA.R2Gn
## -0.256142573 -1.450956141 1.037022668 2.110273941
## ASNS.RPPA AR.RPPA PDK1.RPPA TFRC.RPPA
## 0.238467906 -0.087821743 -0.003536870 0.039119398
## TP53.M CTNNB1.M ACACA.M AR.M
## 0.110847089 0.106800858 0.336451651 0.326972064
## MACC1.M YAP1.g CDH2.g ATM.g
## 0.318500790 0.046830810 0.168355454 0.269535559
## BIRC2.g NOTCH1.g MAPK9.g PCNA.g
## 0.044110774 0.222752101 -0.107384694 -0.067608748
## SMAD4.g CHEK1.g ETS1.g NRG1.g
## 0.005624286 0.266752753 0.416145071 -0.005731907
## NOTCH3.g PGR.g YWHAB.g ANXA1.g
## 0.061887757 0.045125274 -0.097228014 0.342379153
## SNAI2.g SQSTM1.g pathologic_stage pathology_T_stage
## -0.050136984 -0.109466127 0.222822105 0.234326716
##
## $fold3$elasticnet_0.5$dev
## [1] -0.836248
##
## $fold3$elasticnet_0.5$auc
## (Intercept) hsa-mir-130b hsa-mir-199a-2 hsa-mir-199b
## -0.685442353 0.138457472 0.157836025 0.267084550
## hsa-mir-592 hsa-mir-605 hsa-mir-659 hsa-mir-664
## -0.013872412 -0.108907656 -0.007136304 -0.466207034
## hsa-mir-874 AKT1.R2Gn MAPK3.R2Gn CHEK1.R2Gn
## -0.213888497 -0.158349175 -0.355740617 0.286600942
## FOXM1.R2Gn XIAP.R2Gn YWHAB.R2Gn CHGA.R2Gn
## 0.136249219 -0.060509423 -0.150109162 0.013014354
## ETS1.g pathologic_stage pathology_T_stage
## 0.057828320 0.061602025 0.040253755
##
##
## $fold3$lasso
## $fold3$lasso$mse
## [1] -0.836248
##
## $fold3$lasso$dev
## [1] -0.836248
##
## $fold3$lasso$auc
## (Intercept) hsa-mir-129-2 hsa-mir-1296 hsa-mir-1307
## -7.772365251 0.249350070 0.297636812 2.165711267
## hsa-mir-199b hsa-mir-2277 hsa-mir-34a hsa-mir-3647
## 2.534427701 -3.303359853 -0.632918567 -1.506989508
## hsa-mir-372 hsa-mir-3926-1 hsa-mir-590 hsa-mir-592
## 0.314937724 -0.538248154 1.961074362 -0.180937634
## hsa-mir-605 hsa-mir-659 hsa-mir-664 hsa-mir-7-1
## -1.482319432 -2.048879451 -0.743497935 5.904715981
## MRE11A.R2Gn AKT1.R2Gn CDKN1A.R2Gn PEA15.R2Gn
## 7.251105049 -2.171514877 -0.003589982 0.116600148
## MAPK3.R2Gn ACVRL1.R2Gn YBX1.R2Gn ACACA.R2Gn
## -1.532199694 2.205659718 0.403878951 0.094411132
## EEF2K.R2Gn BAX.R2Gn CASP9.R2Gn CHGA.R2Gn
## -0.459786293 -0.688962085 0.829806982 1.423017447
## ASNS.RPPA MAPK9.g ETS1.g SQSTM1.g
## 0.402997745 -0.096926885 0.846511361 -0.001720483
## pathologic_stage pathology_T_stage
## 0.453507516 0.516498771
##
##
##
## $fold5
## $fold5$elasticnet_0.2
## $fold5$elasticnet_0.2$mse
## (Intercept) hsa-mir-125a hsa-mir-130b hsa-mir-135b
## -0.729388804 -0.099991455 0.208339910 0.020981631
## hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-301b
## 0.069947190 0.135626718 0.165027428 0.001946579
## hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-3647 hsa-mir-375
## -0.026893312 -0.013265213 -0.046192039 0.019290454
## hsa-mir-3926-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-592
## -0.029982927 -0.005863953 -0.030460309 -0.028134603
## hsa-mir-605 hsa-mir-659 hsa-mir-664 hsa-mir-7-1
## -0.065945710 -0.059787649 -0.284682008 0.031836392
## hsa-mir-874 AKT1.R2Gn MAPK9.R2Gn MAPK3.R2Gn
## -0.167594900 -0.106040395 -0.040020064 -0.232456337
## YBX1.R2Gn CHEK1.R2Gn EEF2K.R2Gn PIK3R1.R2Gn
## 0.040764783 0.276563583 -0.019407616 -0.007220953
## MSH6.R2Gn PRKAA1.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.030037995 -0.071369713 0.124833138 -0.120311109
## YWHAB.R2Gn CASP9.R2Gn CHGA.R2Gn TFRC.RPPA
## -0.101335719 0.022107296 0.078646434 0.007688925
## ATM.g CHEK1.g ETS1.g pathologic_stage
## 0.003317895 0.003326216 0.052918061 0.045829425
## pathology_T_stage
## 0.039570767
##
## $fold5$elasticnet_0.2$dev
## [1] -0.836248
##
##
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$mse
## [1] -0.836248
##
## $fold5$elasticnet_0.5$dev
## [1] -0.836248
##
##
## $fold5$lasso
## $fold5$lasso$mse
## (Intercept) hsa-mir-199b hsa-mir-605 hsa-mir-664
## -0.28870711 0.19679922 -0.04621114 -0.83213040
## hsa-mir-874 AKT1.R2Gn MAPK3.R2Gn FOXM1.R2Gn
## -0.07909123 -0.02640800 -0.04602342 0.17434211
## YWHAB.R2Gn pathologic_stage
## -0.10674757 0.01222499
##
## $fold5$lasso$dev
## [1] -0.836248
##
##
##
## $fold10
## $fold10$elasticnet_0.2
## $fold10$elasticnet_0.2$mse
## (Intercept) hsa-let-7f-1 hsa-let-7f-2 hsa-mir-106b
## -1.2750044217 -0.1056454914 -0.0090813262 0.0601083761
## hsa-mir-125a hsa-mir-1277 hsa-mir-129-2 hsa-mir-1296
## -0.2263778959 -0.0212167741 0.0457795202 0.0551724575
## hsa-mir-1307 hsa-mir-130b hsa-mir-135b hsa-mir-197
## 0.1030818016 0.3216261162 0.0515951496 0.1038543594
## hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b hsa-mir-2277
## 0.1914084203 0.2622218130 0.2883555459 -0.0464732715
## hsa-mir-301b hsa-mir-3199-1 hsa-mir-320c-2 hsa-mir-34a
## 0.0380535602 -0.1072952887 -0.0502123191 -0.0637601109
## hsa-mir-3647 hsa-mir-3655 hsa-mir-372 hsa-mir-375
## -0.2402346877 -0.0163688558 0.0144356750 0.0546170083
## hsa-mir-3926-1 hsa-mir-3926-2 hsa-mir-3934 hsa-mir-425
## -0.1133039404 -0.0041870552 -0.0002702772 0.0221976574
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-590 hsa-mir-592
## -0.0212232388 -0.0401509369 0.1542697766 -0.0786273589
## hsa-mir-605 hsa-mir-653 hsa-mir-659 hsa-mir-664
## -0.1151543057 -0.0042918627 -0.1827203270 -0.3256797411
## hsa-mir-7-1 hsa-mir-874 MRE11A.R2Gn AKT1.R2Gn
## 0.2626847423 -0.1634560743 0.4243082228 -0.2277108477
## PEA15.R2Gn MAPK9.R2Gn MAPK3.R2Gn ACVRL1.R2Gn
## 0.0322865993 -0.0359925563 -0.4121256152 0.0423359102
## TSC2.R2Gn YBX1.R2Gn CHEK1.R2Gn EEF2K.R2Gn
## -0.0453683245 0.1078556421 0.4101582817 -0.1456199392
## PIK3R1.R2Gn MSH6.R2Gn PRKAA1.R2Gn FOXM1.R2Gn
## -0.0123974856 0.1030376901 -0.1645600451 0.1538144507
## XIAP.R2Gn YWHAB.R2Gn CASP9.R2Gn CHGA.R2Gn
## -0.1147957225 -0.1307486700 0.1564407940 0.2820661029
## ASNS.RPPA TFRC.RPPA YAP1.g ATM.g
## 0.0461333900 0.0200968227 0.0104253976 0.0497608041
## BIRC2.g MAPK9.g PCNA.g CHEK1.g
## 0.0103757012 -0.0015915140 -0.0202581363 0.0497075363
## ETS1.g NOTCH3.g PGR.g YWHAB.g
## 0.1003490714 0.0140747310 0.0103385272 -0.0247295849
## ANXA1.g SQSTM1.g pathologic_stage pathology_T_stage
## 0.0463202334 -0.0015961411 0.0736597452 0.0630713941
##
## $fold10$elasticnet_0.2$dev
## (Intercept) hsa-let-7f-1 hsa-let-7f-2 hsa-mir-106b
## -1.363746577 -0.127144193 -0.026490410 0.075048015
## hsa-mir-125a hsa-mir-1277 hsa-mir-129-1 hsa-mir-129-2
## -0.245703678 -0.046748076 0.001451632 0.055730284
## hsa-mir-1296 hsa-mir-1307 hsa-mir-130b hsa-mir-135b
## 0.075081609 0.124486937 0.334503327 0.056214936
## hsa-mir-197 hsa-mir-199a-1 hsa-mir-199a-2 hsa-mir-199b
## 0.118884777 0.211574535 0.282681944 0.308071197
## hsa-mir-2277 hsa-mir-301b hsa-mir-3199-1 hsa-mir-320c-2
## -0.082137182 0.042840992 -0.117823756 -0.055784909
## hsa-mir-34a hsa-mir-3647 hsa-mir-3655 hsa-mir-372
## -0.075383660 -0.270732618 -0.019625419 0.028592680
## hsa-mir-375 hsa-mir-3909 hsa-mir-3926-1 hsa-mir-3926-2
## 0.055255984 -0.005084634 -0.128279940 -0.010910663
## hsa-mir-3934 hsa-mir-425 hsa-mir-513a-2 hsa-mir-513b
## -0.006456341 0.049816877 -0.023006509 -0.040409771
## hsa-mir-590 hsa-mir-592 hsa-mir-605 hsa-mir-653
## 0.201359436 -0.085398714 -0.122868934 -0.010428513
## hsa-mir-659 hsa-mir-664 hsa-mir-7-1 hsa-mir-874
## -0.205177074 -0.326969171 0.303567612 -0.157678411
## MRE11A.R2Gn AKT1.R2Gn PEA15.R2Gn MAPK9.R2Gn
## 0.523315672 -0.247893660 0.043995877 -0.031312139
## MAPK3.R2Gn ACVRL1.R2Gn TSC2.R2Gn YBX1.R2Gn
## -0.441914231 0.069915393 -0.066973081 0.113820793
## CHEK1.R2Gn EEF2K.R2Gn PIK3R1.R2Gn BCL2L1.R2Gn
## 0.435355653 -0.163094953 -0.012036551 -0.007923252
## MSH6.R2Gn PRKAA1.R2Gn FOXM1.R2Gn XIAP.R2Gn
## 0.111081465 -0.172967037 0.157593371 -0.103494146
## YWHAB.R2Gn BAX.R2Gn TFRC.R2Gn CASP9.R2Gn
## -0.135707193 -0.039130371 0.001506770 0.174146802
## CHGA.R2Gn ASNS.RPPA AR.RPPA TFRC.RPPA
## 0.321811489 0.054882397 -0.006117451 0.021768195
## YAP1.g ATM.g BIRC2.g MAPK9.g
## 0.014848084 0.056527391 0.014802137 -0.005117267
## PCNA.g CHEK1.g ETS1.g NOTCH3.g
## -0.023507077 0.056490344 0.107042339 0.019275337
## PGR.g YWHAB.g ANXA1.g SQSTM1.g
## 0.014770020 -0.030320819 0.059024427 -0.005125231
## pathologic_stage pathology_T_stage
## 0.076774845 0.066523877
##
##
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$mse
## [1] -0.836248
##
## $fold10$elasticnet_0.5$dev
## [1] -0.836248
##
##
## $fold10$lasso
## $fold10$lasso$mse
## [1] -0.836248
##
## $fold10$lasso$dev
## [1] -0.8362481. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
#Mutations and gistict for glmnet only
out.M = variable.list[endsWith(variable.list, ".M")]
out.g = variable.list[endsWith(variable.list, ".g")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA,
"Mutations" = out.M,
"gistict" = out.g)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
M.genes = str_remove(multiomics.list[[4]], ".M")
g.genes = str_remove(multiomics.list[[5]], ".g")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
out = as.character(unique(out1))
out
}geneNames <- list("3F_0.5_MSE"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$mse)),
"3F_0.5_AUC"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$auc)),
"3F_1_AUC"=multiomics.to.GENES(names(sel.features$fold3$lasso$auc)),
"5F_0.2_MSE"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.2$mse)),
"5F_1_MSE"=multiomics.to.GENES(names(sel.features$fold5$lasso$mse), drop.miRNA = T ), # 4 microRNAs dropped
"10F_0.2_MSE"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.2$mse)),
"10F_0.2_DEV"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.2$dev)))## Searching mirecords ...
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## Searching tarbase ...geneNames## $`3F_0.5_MSE`
## [1] "NOTCH1" "ERBB2" "NF2" "KRAS" "CCND1" "AKT1" "BCL2L1"
## [8] "AR" "FASN" "RB1" "PIK3R1" "XIAP" "CHEK1" "IGF1R"
## [15] "SRSF1" "TUBA1B" "CDK1" "YBX1" "BECN1" "ERBB3" "FOXO3"
## [22] "ACACA" "E2F1" "MYC" "BCL2L11" "RAF1" "XBP1" "AKT3"
## [29] "EEF2" "EIF4G1" "GSK3B" "MSH6" "ITGA2" "KDR" "MRE11A"
## [36] "ASNS" "CDKN1A" "PEA15" "MAPK1" "STK11" "ADAR" "MAPK3"
## [43] "ACVRL1" "TSC2" "JUN" "RAB11B" "EEF2K" "DVL3" "PRKAA1"
## [50] "FOXM1" "YWHAB" "BAX" "CASP9" "CHGA" "PDK1" "TFRC"
## [57] "TP53" "CTNNB1" "MACC1" "YAP1" "CDH2" "ATM" "BIRC2"
## [64] "MAPK9" "PCNA" "SMAD4" "ETS1" "NRG1" "NOTCH3" "PGR"
## [71] "ANXA1" "SNAI2" "SQSTM1"
##
## $`3F_0.5_AUC`
## [1] "ERBB3" "FOXO3" "IGF1R" "ACACA" "CCND1" "MYC" "EIF4G1" "AKT1"
## [9] "MAPK3" "CHEK1" "FOXM1" "XIAP" "YWHAB" "CHGA" "ETS1"
##
## $`3F_1_AUC`
## [1] "ERBB3" "FOXO3" "IGF1R" "ACACA" "CCND1" "MYC" "EIF4G1" "MRE11A"
## [9] "AKT1" "CDKN1A" "PEA15" "MAPK3" "ACVRL1" "YBX1" "EEF2K" "BAX"
## [17] "CASP9" "CHGA" "ASNS" "MAPK9" "ETS1" "SQSTM1"
##
## $`5F_0.2_MSE`
## [1] "ERBB3" "FOXO3" "IGF1R" "ACACA" "BCL2" "ERBB2" "AXL"
## [8] "BAK1" "MYC" "CASP3" "BCL2L11" "TP53" "YAP1" "YWHAZ"
## [15] "STAT3" "PARP1" "XIAP" "CTNNB1" "PRDX1" "PDK1" "PIK3CA"
## [22] "PRKCA" "MAPK3" "TFRC" "TGM2" "CCND1" "EIF4G1" "MYH9"
## [29] "CDKN1A" "IRS1" "JUN" "RAF1" "TYMS" "ANXA7" "CLDN7"
## [36] "CTNNA1" "YBX1" "RPS6" "SRSF1" "NDRG1" "PECAM1" "YWHAB"
## [43] "SETD2" "AKT1" "MAPK9" "CHEK1" "EEF2K" "PIK3R1" "MSH6"
## [50] "PRKAA1" "FOXM1" "CASP9" "CHGA" "ATM" "ETS1"
##
## $`5F_1_MSE`
## [1] "AKT1" "MAPK3" "FOXM1" "YWHAB"
##
## $`10F_0.2_MSE`
## [1] "ERBB3" "FOXO3" "IGF1R" "ACACA" "BCL2" "ERBB2" "AXL"
## [8] "BAK1" "MYC" "CASP3" "BCL2L11" "TP53" "YAP1" "YWHAZ"
## [15] "STAT3" "PARP1" "XIAP" "CTNNB1" "PRDX1" "PDK1" "PIK3CA"
## [22] "PRKCA" "MAPK3" "TFRC" "TGM2" "MYH9" "CCND1" "CDKN1A"
## [29] "IRS1" "JUN" "RAF1" "TYMS" "ANXA7" "CLDN7" "CTNNA1"
## [36] "EIF4G1" "YBX1" "RPS6" "SRSF1" "NDRG1" "PECAM1" "YWHAB"
## [43] "SETD2" "MRE11A" "AKT1" "PEA15" "MAPK9" "ACVRL1" "TSC2"
## [50] "CHEK1" "EEF2K" "PIK3R1" "MSH6" "PRKAA1" "FOXM1" "CASP9"
## [57] "CHGA" "ASNS" "ATM" "BIRC2" "PCNA" "ETS1" "NOTCH3"
## [64] "PGR" "ANXA1" "SQSTM1"
##
## $`10F_0.2_DEV`
## [1] "RB1" "ERBB3" "FOXO3" "IGF1R" "ACACA" "BCL2" "ERBB2"
## [8] "AXL" "BAK1" "MYC" "CASP3" "BCL2L11" "TP53" "YAP1"
## [15] "YWHAZ" "STAT3" "PARP1" "XIAP" "CTNNB1" "PRDX1" "PDK1"
## [22] "PIK3CA" "PRKCA" "MAPK3" "TFRC" "TGM2" "MYH9" "CCND1"
## [29] "CDKN1A" "IRS1" "JUN" "RAF1" "TYMS" "ANXA7" "CLDN7"
## [36] "CTNNA1" "EIF4G1" "YBX1" "RPS6" "SRSF1" "NDRG1" "PECAM1"
## [43] "YWHAB" "SETD2" "MRE11A" "AKT1" "PEA15" "MAPK9" "ACVRL1"
## [50] "TSC2" "CHEK1" "EEF2K" "PIK3R1" "BCL2L1" "MSH6" "PRKAA1"
## [57] "FOXM1" "BAX" "CASP9" "CHGA" "ASNS" "AR" "ATM"
## [64] "BIRC2" "PCNA" "ETS1" "NOTCH3" "PGR" "ANXA1" "SQSTM1"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/73
## GO:0003824 GO:0003824 catalytic activity 34 34/73
## GO:0005198 GO:0005198 structural molecule activity 1 1/73
## GO:0005215 GO:0005215 transporter activity 2 2/73
## GO:0005488 GO:0005488 binding 71 71/73
## GO:0009055 GO:0009055 electron transfer activity 0 0/73
## geneID
## GO:0003774
## GO:0003824 ERBB2/KRAS/CCND1/AKT1/FASN/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/CDK1/ACACA/RAF1/AKT3/EEF2/GSK3B/MSH6/KDR/ASNS/CDKN1A/MAPK1/STK11/ADAR/MAPK3/ACVRL1/RAB11B/EEF2K/PRKAA1/CASP9/PDK1/ATM/BIRC2/MAPK9/PCNA
## GO:0005198 TUBA1B
## GO:0005215 IGF1R/BAX
## GO:0005488 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/73
## GO:0002376 GO:0002376 immune system process 32 32/73
## GO:0008152 GO:0008152 metabolic process 66 66/73
## GO:0009987 GO:0009987 cellular process 72 72/73
## GO:0016032 GO:0016032 viral process 10 10/73
## GO:0022414 GO:0022414 reproductive process 19 19/73
## geneID
## GO:0000003 NOTCH1/AKT1/BCL2L1/AR/RB1/IGF1R/CDK1/FOXO3/BCL2L11/MSH6/ITGA2/KDR/STK11/BAX/CTNNB1/ATM/PCNA/SMAD4/PGR
## GO:0002376 NOTCH1/ERBB2/AKT1/RB1/PIK3R1/XIAP/IGF1R/BECN1/FOXO3/MYC/BCL2L11/RAF1/XBP1/MSH6/ITGA2/CDKN1A/MAPK1/STK11/ADAR/MAPK3/BAX/CHGA/TFRC/TP53/CTNNB1/ATM/BIRC2/MAPK9/ETS1/ANXA1/SNAI2/SQSTM1
## GO:0008152 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0009987 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/CHGA/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0016032 NOTCH1/AKT1/CDK1/BECN1/GSK3B/ITGA2/ADAR/JUN/TFRC/TP53
## GO:0022414 NOTCH1/AKT1/BCL2L1/AR/RB1/IGF1R/CDK1/FOXO3/BCL2L11/MSH6/ITGA2/KDR/STK11/BAX/CTNNB1/ATM/PCNA/SMAD4/PGR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 52 52/73
## GO:0044423 GO:0044423 virion component 0 0/73
## GO:0110165 GO:0110165 cellular anatomical entity 72 72/73
## geneID
## GO:0032991 NOTCH1/ERBB2/CCND1/AKT1/BCL2L1/AR/RB1/PIK3R1/CHEK1/IGF1R/SRSF1/CDK1/YBX1/BECN1/ERBB3/FOXO3/E2F1/MYC/BCL2L11/XBP1/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/CDKN1A/PEA15/STK11/ADAR/ACVRL1/TSC2/JUN/DVL3/PRKAA1/FOXM1/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/YAP1/CDH2/ATM/BIRC2/PCNA/SMAD4/ETS1/NOTCH3/PGR/SNAI2
## GO:0044423
## GO:0110165 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/CHGA/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/15
## GO:0003824 GO:0003824 catalytic activity 7 7/15
## GO:0005198 GO:0005198 structural molecule activity 0 0/15
## GO:0005215 GO:0005215 transporter activity 1 1/15
## GO:0005488 GO:0005488 binding 14 14/15
## GO:0009055 GO:0009055 electron transfer activity 0 0/15
## geneID
## GO:0003774
## GO:0003824 IGF1R/ACACA/CCND1/AKT1/MAPK3/CHEK1/XIAP
## GO:0005198
## GO:0005215 IGF1R
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/ETS1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 3 3/15
## GO:0002376 GO:0002376 immune system process 8 8/15
## GO:0008152 GO:0008152 metabolic process 14 14/15
## GO:0009987 GO:0009987 cellular process 15 15/15
## GO:0016032 GO:0016032 viral process 1 1/15
## GO:0022414 GO:0022414 reproductive process 3 3/15
## geneID
## GO:0000003 FOXO3/IGF1R/AKT1
## GO:0002376 FOXO3/IGF1R/MYC/AKT1/MAPK3/XIAP/CHGA/ETS1
## GO:0008152 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/ETS1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/CHGA/ETS1
## GO:0016032 AKT1
## GO:0022414 FOXO3/IGF1R/AKT1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 10 10/15
## GO:0044423 GO:0044423 virion component 0 0/15
## GO:0110165 GO:0110165 cellular anatomical entity 15 15/15
## geneID
## GO:0032991 ERBB3/FOXO3/IGF1R/CCND1/MYC/EIF4G1/AKT1/CHEK1/FOXM1/ETS1
## GO:0044423
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/CHGA/ETS1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/22
## GO:0003824 GO:0003824 catalytic activity 11 11/22
## GO:0005198 GO:0005198 structural molecule activity 0 0/22
## GO:0005215 GO:0005215 transporter activity 2 2/22
## GO:0005488 GO:0005488 binding 20 20/22
## GO:0009055 GO:0009055 electron transfer activity 0 0/22
## geneID
## GO:0003774
## GO:0003824 IGF1R/ACACA/CCND1/AKT1/CDKN1A/MAPK3/ACVRL1/EEF2K/CASP9/ASNS/MAPK9
## GO:0005198
## GO:0005215 IGF1R/BAX
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/ASNS/MAPK9/ETS1/SQSTM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/22
## GO:0002376 GO:0002376 immune system process 11 11/22
## GO:0008152 GO:0008152 metabolic process 19 19/22
## GO:0009987 GO:0009987 cellular process 21 21/22
## GO:0016032 GO:0016032 viral process 1 1/22
## GO:0022414 GO:0022414 reproductive process 4 4/22
## geneID
## GO:0000003 FOXO3/IGF1R/AKT1/BAX
## GO:0002376 FOXO3/IGF1R/MYC/AKT1/CDKN1A/MAPK3/BAX/CHGA/MAPK9/ETS1/SQSTM1
## GO:0008152 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/ASNS/MAPK9/ETS1/SQSTM1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/CHGA/ASNS/MAPK9/ETS1/SQSTM1
## GO:0016032 AKT1
## GO:0022414 FOXO3/IGF1R/AKT1/BAX
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 14 14/22
## GO:0044423 GO:0044423 virion component 0 0/22
## GO:0110165 GO:0110165 cellular anatomical entity 21 21/22
## geneID
## GO:0032991 ERBB3/FOXO3/IGF1R/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/ACVRL1/YBX1/BAX/CASP9/ETS1
## GO:0044423
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/CHGA/ASNS/MAPK9/ETS1/SQSTM1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/55
## GO:0003824 GO:0003824 catalytic activity 27 27/55
## GO:0005198 GO:0005198 structural molecule activity 3 3/55
## GO:0005215 GO:0005215 transporter activity 3 3/55
## GO:0005488 GO:0005488 binding 54 54/55
## GO:0009055 GO:0009055 electron transfer activity 0 0/55
## geneID
## GO:0003774 MYH9
## GO:0003824 IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ATM
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 IGF1R/BCL2/BAK1
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 16 16/55
## GO:0002376 GO:0002376 immune system process 33 33/55
## GO:0008152 GO:0008152 metabolic process 50 50/55
## GO:0009987 GO:0009987 cellular process 55 55/55
## GO:0016032 GO:0016032 viral process 6 6/55
## GO:0022414 GO:0022414 reproductive process 15 15/55
## geneID
## GO:0000003 FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM
## GO:0002376 FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/CHGA/ATM/ETS1
## GO:0008152 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ATM/ETS1
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414 FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 40 40/55
## GO:0044423 GO:0044423 virion component 0 0/55
## GO:0110165 GO:0110165 cellular anatomical entity 55 55/55
## geneID
## GO:0032991 ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/CTNNA1/YBX1/RPS6/SRSF1/PECAM1/AKT1/CHEK1/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0044423
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ATM/ETS1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/4
## GO:0003824 GO:0003824 catalytic activity 2 2/4
## GO:0005198 GO:0005198 structural molecule activity 0 0/4
## GO:0005215 GO:0005215 transporter activity 0 0/4
## GO:0005488 GO:0005488 binding 4 4/4
## GO:0009055 GO:0009055 electron transfer activity 0 0/4
## geneID
## GO:0003774
## GO:0003824 AKT1/MAPK3
## GO:0005198
## GO:0005215
## GO:0005488 AKT1/MAPK3/FOXM1/YWHAB
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 1 1/4
## GO:0002376 GO:0002376 immune system process 2 2/4
## GO:0008152 GO:0008152 metabolic process 4 4/4
## GO:0009987 GO:0009987 cellular process 4 4/4
## GO:0016032 GO:0016032 viral process 1 1/4
## GO:0022414 GO:0022414 reproductive process 1 1/4
## geneID
## GO:0000003 AKT1
## GO:0002376 AKT1/MAPK3
## GO:0008152 AKT1/MAPK3/FOXM1/YWHAB
## GO:0009987 AKT1/MAPK3/FOXM1/YWHAB
## GO:0016032 AKT1
## GO:0022414 AKT1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 2 2/4
## GO:0044423 GO:0044423 virion component 0 0/4
## GO:0110165 GO:0110165 cellular anatomical entity 4 4/4
## geneID
## GO:0032991 AKT1/FOXM1
## GO:0044423
## GO:0110165 AKT1/MAPK3/FOXM1/YWHAB
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/66
## GO:0003824 GO:0003824 catalytic activity 31 31/66
## GO:0005198 GO:0005198 structural molecule activity 3 3/66
## GO:0005215 GO:0005215 transporter activity 3 3/66
## GO:0005488 GO:0005488 binding 64 64/66
## GO:0009055 GO:0009055 electron transfer activity 0 0/66
## geneID
## GO:0003774 MYH9
## GO:0003824 IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ASNS/ATM/BIRC2/PCNA
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 IGF1R/BCL2/BAK1
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 18 18/66
## GO:0002376 GO:0002376 immune system process 36 36/66
## GO:0008152 GO:0008152 metabolic process 59 59/66
## GO:0009987 GO:0009987 cellular process 65 65/66
## GO:0016032 GO:0016032 viral process 6 6/66
## GO:0022414 GO:0022414 reproductive process 17 17/66
## geneID
## GO:0000003 FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM/PCNA/PGR
## GO:0002376 FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/CHGA/ATM/BIRC2/ETS1/ANXA1/SQSTM1
## GO:0008152 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414 FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM/PCNA/PGR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 47 47/66
## GO:0044423 GO:0044423 virion component 0 0/66
## GO:0110165 GO:0110165 cellular anatomical entity 65 65/66
## geneID
## GO:0032991 ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/PEA15/ACVRL1/TSC2/CHEK1/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR
## GO:0044423
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/70
## GO:0003824 GO:0003824 catalytic activity 31 31/70
## GO:0005198 GO:0005198 structural molecule activity 3 3/70
## GO:0005215 GO:0005215 transporter activity 4 4/70
## GO:0005488 GO:0005488 binding 68 68/70
## GO:0009055 GO:0009055 electron transfer activity 0 0/70
## geneID
## GO:0003774 MYH9
## GO:0003824 IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ASNS/ATM/BIRC2/PCNA
## GO:0005198 CLDN7/CTNNA1/RPS6
## GO:0005215 IGF1R/BCL2/BAK1/BAX
## GO:0005488 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 22 22/70
## GO:0002376 GO:0002376 immune system process 38 38/70
## GO:0008152 GO:0008152 metabolic process 62 62/70
## GO:0009987 GO:0009987 cellular process 69 69/70
## GO:0016032 GO:0016032 viral process 6 6/70
## GO:0022414 GO:0022414 reproductive process 21 21/70
## geneID
## GO:0000003 RB1/FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/BCL2L1/MSH6/BAX/AR/ATM/PCNA/PGR
## GO:0002376 RB1/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/BAX/CHGA/ATM/BIRC2/ETS1/ANXA1/SQSTM1
## GO:0008152 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/BAX/CASP9/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009987 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/CHGA/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0016032 BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414 RB1/FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/BCL2L1/MSH6/BAX/AR/ATM/PCNA/PGR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 51 51/70
## GO:0044423 GO:0044423 virion component 0 0/70
## GO:0110165 GO:0110165 cellular anatomical entity 69 69/70
## geneID
## GO:0032991 RB1/ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/PEA15/ACVRL1/TSC2/CHEK1/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR
## GO:0044423
## GO:0110165 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/CHGA/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 14/71
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 4/71
## GO:0106310 GO:0106310 protein serine kinase activity 12/71
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 13/71
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 10/71
## GO:0001221 GO:0001221 transcription coregulator binding 7/71
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 7.049681e-10 1.783577e-07 8.009065e-08
## GO:0043125 5/18522 9.881314e-10 1.783577e-07 8.009065e-08
## GO:0106310 363/18522 1.213357e-08 1.460074e-06 6.556388e-07
## GO:0140297 478/18522 2.844093e-08 2.566794e-06 1.152606e-06
## GO:0031625 305/18522 2.405162e-07 1.606434e-05 7.213614e-06
## GO:0001221 114/18522 2.669974e-07 1.606434e-05 7.213614e-06
## geneID
## GO:0004674 AKT1/CHEK1/CDK1/RAF1/AKT3/GSK3B/MAPK1/STK11/MAPK3/ACVRL1/EEF2K/PRKAA1/ATM/MAPK9
## GO:0043125 ERBB2/PIK3R1/ERBB3/NRG1
## GO:0106310 AKT1/CHEK1/CDK1/RAF1/AKT3/GSK3B/MAPK1/STK11/MAPK3/PRKAA1/ATM/MAPK9
## GO:0140297 AR/RB1/E2F1/MYC/GSK3B/MAPK3/JUN/TP53/CTNNB1/YAP1/PCNA/SMAD4/ETS1
## GO:0031625 RB1/TUBA1B/BECN1/ERBB3/GSK3B/CDKN1A/JUN/TP53/CTNNB1/SQSTM1
## GO:0001221 AR/FOXO3/MYC/CTNNB1/SMAD4/ETS1/PGR
## Count
## GO:0004674 14
## GO:0043125 4
## GO:0106310 12
## GO:0140297 13
## GO:0031625 10
## GO:0001221 7
## ID Description GeneRatio
## GO:0048732 GO:0048732 gland development 21/72
## GO:0050673 GO:0050673 epithelial cell proliferation 21/72
## GO:0097193 GO:0097193 intrinsic apoptotic signaling pathway 18/72
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 17/72
## GO:0104004 GO:0104004 cellular response to environmental stimulus 17/72
## GO:0070482 GO:0070482 response to oxygen levels 17/72
## BgRatio pvalue p.adjust qvalue
## GO:0048732 449/18888 1.255727e-17 4.568333e-14 1.896808e-14
## GO:0050673 482/18888 5.275417e-17 9.595983e-14 3.984328e-14
## GO:0097193 319/18888 1.407215e-16 1.706482e-13 7.085449e-14
## GO:0071214 334/18888 6.054784e-15 4.405461e-12 1.829182e-12
## GO:0104004 334/18888 6.054784e-15 4.405461e-12 1.829182e-12
## GO:0070482 354/18888 1.575864e-14 9.554988e-12 3.967306e-12
## geneID
## GO:0048732 NOTCH1/CCND1/AKT1/AR/FASN/SRSF1/BCL2L11/RAF1/XBP1/ITGA2/MAPK1/STK11/MAPK3/BAX/CTNNB1/ATM/PCNA/SMAD4/NRG1/PGR/SNAI2
## GO:0050673 NOTCH1/ERBB2/CCND1/AKT1/BCL2L1/AR/RB1/MYC/RAF1/XBP1/AKT3/KDR/CDKN1A/MAPK1/STK11/ACVRL1/BAX/CTNNB1/YAP1/PGR/SNAI2
## GO:0097193 AKT1/BCL2L1/PIK3R1/BECN1/E2F1/MYC/BCL2L11/XBP1/MSH6/CDKN1A/STK11/BAX/CASP9/PDK1/TP53/CTNNB1/ATM/SNAI2
## GO:0071214 BCL2L1/PIK3R1/CHEK1/IGF1R/MYC/ITGA2/CDKN1A/STK11/MAPK3/RAB11B/BAX/CASP9/TP53/YAP1/ATM/PCNA/SNAI2
## GO:0104004 BCL2L1/PIK3R1/CHEK1/IGF1R/MYC/ITGA2/CDKN1A/STK11/MAPK3/RAB11B/BAX/CASP9/TP53/YAP1/ATM/PCNA/SNAI2
## GO:0070482 NOTCH1/AKT1/BECN1/FOXO3/MYC/ITGA2/CDKN1A/ACVRL1/EEF2K/PRKAA1/CASP9/PDK1/TFRC/TP53/ATM/BIRC2/SMAD4
## Count
## GO:0048732 21
## GO:0050673 21
## GO:0097193 18
## GO:0071214 17
## GO:0104004 17
## GO:0070482 17
## ID
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
## GO:0005741 GO:0005741
## GO:0000307 GO:0000307
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## Description
## GO:1902911 protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005741 mitochondrial outer membrane
## GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0031968 organelle outer membrane
## GO:0019867 outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902911 8/72 150/19894 6.892704e-08 1.847245e-05 1.052044e-05
## GO:0061695 10/72 308/19894 1.570194e-07 2.104060e-05 1.198306e-05
## GO:0005741 8/72 219/19894 1.240321e-06 1.108020e-04 6.310407e-05
## GO:0000307 5/72 56/19894 1.784398e-06 1.195546e-04 6.808886e-05
## GO:0031968 8/72 248/19894 3.133960e-06 1.473968e-04 8.394557e-05
## GO:0019867 8/72 250/19894 3.325891e-06 1.473968e-04 8.394557e-05
## geneID Count
## GO:1902911 CCND1/RB1/IGF1R/CDK1/CDKN1A/STK11/PRKAA1/PCNA 8
## GO:0061695 CCND1/RB1/PIK3R1/IGF1R/CDK1/BECN1/CDKN1A/STK11/PRKAA1/PCNA 10
## GO:0005741 KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR 8
## GO:0000307 CCND1/RB1/CDK1/CDKN1A/PCNA 5
## GO:0031968 KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR 8
## GO:0019867 KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR 8
## ID Description GeneRatio
## GO:0019887 GO:0019887 protein kinase regulator activity 4/14
## GO:0019207 GO:0019207 kinase regulator activity 4/14
## GO:0001221 GO:0001221 transcription coregulator binding 3/14
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 2/14
## GO:0004860 GO:0004860 protein kinase inhibitor activity 2/14
## GO:0003989 GO:0003989 acetyl-CoA carboxylase activity 1/14
## BgRatio pvalue p.adjust qvalue
## GO:0019887 232/18522 2.175551e-05 0.002107870 0.0007465156
## GO:0019207 270/18522 3.939943e-05 0.002107870 0.0007465156
## GO:0001221 114/18522 7.867077e-05 0.002805924 0.0009937361
## GO:0045309 59/18522 8.856817e-04 0.017119598 0.0060630154
## GO:0004860 73/18522 1.352161e-03 0.017119598 0.0060630154
## GO:0003989 2/18522 1.511185e-03 0.017119598 0.0060630154
## geneID Count
## GO:0019887 ERBB3/CCND1/AKT1/YWHAB 4
## GO:0019207 ERBB3/CCND1/AKT1/YWHAB 4
## GO:0001221 FOXO3/MYC/ETS1 3
## GO:0045309 MAPK3/YWHAB 2
## GO:0004860 AKT1/YWHAB 2
## GO:0003989 ACACA 1
## ID Description GeneRatio
## GO:0072331 GO:0072331 signal transduction by p53 class mediator 5/15
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 5/15
## GO:0051347 GO:0051347 positive regulation of transferase activity 6/15
## GO:0044772 GO:0044772 mitotic cell cycle phase transition 6/15
## GO:0097306 GO:0097306 cellular response to alcohol 4/15
## GO:0097305 GO:0097305 response to alcohol 5/15
## BgRatio pvalue p.adjust qvalue
## GO:0072331 177/18888 1.900682e-07 0.0001165852 5.017132e-05
## GO:0042770 188/18888 2.565495e-07 0.0001165852 5.017132e-05
## GO:0051347 376/18888 2.571731e-07 0.0001165852 5.017132e-05
## GO:0044772 451/18888 7.473915e-07 0.0002460387 1.058804e-04
## GO:0097306 106/18888 1.219604e-06 0.0002460387 1.058804e-04
## GO:0097305 259/18888 1.251969e-06 0.0002460387 1.058804e-04
## geneID Count
## GO:0072331 FOXO3/MYC/AKT1/CHEK1/FOXM1 5
## GO:0042770 FOXO3/CCND1/MAPK3/CHEK1/FOXM1 5
## GO:0051347 ERBB3/IGF1R/CCND1/MYC/AKT1/MAPK3 6
## GO:0044772 CCND1/MYC/EIF4G1/AKT1/CHEK1/FOXM1 6
## GO:0097306 FOXO3/IGF1R/ACACA/AKT1 4
## GO:0097305 FOXO3/IGF1R/ACACA/EIF4G1/AKT1 5
## ID Description
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0038143 GO:0038143 ERBB3:ERBB2 complex
## GO:0071943 GO:0071943 Myc-Max complex
## GO:0097128 GO:0097128 cyclin D1-CDK4 complex
## GO:0005901 GO:0005901 caveola
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0017053 3/15 77/19894 2.453163e-05 0.001643619 0.001084556
## GO:0090571 2/15 15/19894 5.540208e-05 0.001855970 0.001224678
## GO:0038143 1/15 2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0071943 1/15 2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0097128 1/15 2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0005901 2/15 82/19894 1.701905e-03 0.019004610 0.012540356
## geneID Count
## GO:0017053 FOXO3/CCND1/MYC 3
## GO:0090571 FOXO3/MYC 2
## GO:0038143 ERBB3 1
## GO:0071943 MYC 1
## GO:0097128 CCND1 1
## GO:0005901 IGF1R/MAPK3 2
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/20
## GO:0019887 GO:0019887 protein kinase regulator activity 4/20
## GO:0004707 GO:0004707 MAP kinase activity 2/20
## GO:0019207 GO:0019207 kinase regulator activity 4/20
## GO:0001221 GO:0001221 transcription coregulator binding 3/20
## GO:0030295 GO:0030295 protein kinase activator activity 3/20
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 7.408307e-05 0.006103321 0.002264769
## GO:0019887 232/18522 9.925604e-05 0.006103321 0.002264769
## GO:0004707 16/18522 1.317264e-04 0.006103321 0.002264769
## GO:0019207 270/18522 1.779924e-04 0.006185235 0.002295165
## GO:0001221 114/18522 2.398379e-04 0.006667495 0.002474118
## GO:0030295 129/18522 3.450128e-04 0.006825483 0.002532743
## geneID Count
## GO:0004674 AKT1/MAPK3/ACVRL1/EEF2K/MAPK9 5
## GO:0019887 ERBB3/CCND1/AKT1/CDKN1A 4
## GO:0004707 MAPK3/MAPK9 2
## GO:0019207 ERBB3/CCND1/AKT1/CDKN1A 4
## GO:0001221 FOXO3/MYC/ETS1 3
## GO:0030295 ERBB3/CCND1/CDKN1A 3
## ID Description GeneRatio
## GO:0009411 GO:0009411 response to UV 6/21
## GO:0031667 GO:0031667 response to nutrient levels 8/21
## GO:0070482 GO:0070482 response to oxygen levels 7/21
## GO:1901655 GO:1901655 cellular response to ketone 5/21
## GO:1901654 GO:1901654 response to ketone 6/21
## GO:0051347 GO:0051347 positive regulation of transferase activity 7/21
## BgRatio pvalue p.adjust qvalue
## GO:0009411 154/18888 1.306671e-08 2.247474e-05 9.504314e-06
## GO:0031667 490/18888 2.930357e-08 2.520107e-05 1.065725e-05
## GO:0070482 354/18888 7.101610e-08 3.070923e-05 1.298658e-05
## GO:1901655 107/18888 1.005224e-07 3.070923e-05 1.298658e-05
## GO:1901654 217/18888 1.008309e-07 3.070923e-05 1.298658e-05
## GO:0051347 376/18888 1.071252e-07 3.070923e-05 1.298658e-05
## geneID Count
## GO:0009411 CCND1/MYC/AKT1/CDKN1A/BAX/CASP9 6
## GO:0031667 FOXO3/IGF1R/EIF4G1/AKT1/CDKN1A/MAPK3/BAX/ASNS 8
## GO:0070482 FOXO3/MYC/AKT1/CDKN1A/ACVRL1/EEF2K/CASP9 7
## GO:1901655 FOXO3/IGF1R/ACACA/AKT1/CASP9 5
## GO:1901654 FOXO3/IGF1R/ACACA/AKT1/CDKN1A/CASP9 6
## GO:0051347 ERBB3/IGF1R/CCND1/MYC/AKT1/CDKN1A/MAPK3 7
## ID Description
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:1902911 GO:1902911 protein kinase complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0038143 GO:0038143 ERBB3:ERBB2 complex
## GO:0070557 GO:0070557 PCNA-p21 complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0017053 3/21 77/19894 7.051822e-05 0.005525745 0.002908287
## GO:0090571 2/21 15/19894 1.105149e-04 0.005525745 0.002908287
## GO:1902911 3/21 150/19894 5.057831e-04 0.016859436 0.008873387
## GO:0000307 2/21 56/19894 1.579160e-03 0.023334521 0.012281327
## GO:0038143 1/21 2/19894 2.110128e-03 0.023334521 0.012281327
## GO:0070557 1/21 2/19894 2.110128e-03 0.023334521 0.012281327
## geneID Count
## GO:0017053 FOXO3/CCND1/MYC 3
## GO:0090571 FOXO3/MYC 2
## GO:1902911 IGF1R/CCND1/CDKN1A 3
## GO:0000307 CCND1/CDKN1A 2
## GO:0038143 ERBB3 1
## GO:0070557 CDKN1A 1
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 11/54
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 3/54
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 10/54
## GO:0035173 GO:0035173 histone kinase activity 4/54
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 5/54
## GO:0043548 GO:0043548 phosphatidylinositol 3-kinase binding 4/54
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 1.060015e-07 3.360246e-05 1.539811e-05
## GO:0043125 5/18522 2.332834e-07 3.697542e-05 1.694374e-05
## GO:0004674 427/18522 3.690298e-07 3.899414e-05 1.786881e-05
## GO:0035173 23/18522 5.482580e-07 4.120201e-05 1.888055e-05
## GO:0045309 59/18522 7.740765e-07 4.120201e-05 1.888055e-05
## GO:0043548 25/18522 7.798488e-07 4.120201e-05 1.888055e-05
## geneID Count
## GO:0140297 BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/ETS1 11
## GO:0043125 ERBB3/ERBB2/PIK3R1 3
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/EEF2K/PRKAA1/ATM 10
## GO:0035173 PRKCA/CHEK1/PRKAA1/ATM 4
## GO:0045309 YWHAZ/MAPK3/IRS1/YWHAB/PIK3R1 5
## GO:0043548 IGF1R/AXL/IRS1/PIK3R1 4
## ID Description GeneRatio
## GO:0009411 GO:0009411 response to UV 13/55
## GO:0097193 GO:0097193 intrinsic apoptotic signaling pathway 15/55
## GO:0010332 GO:0010332 response to gamma radiation 9/55
## GO:0051402 GO:0051402 neuron apoptotic process 14/55
## GO:0043523 GO:0043523 regulation of neuron apoptotic process 13/55
## GO:0097305 GO:0097305 response to alcohol 13/55
## BgRatio pvalue p.adjust qvalue
## GO:0009411 154/18888 4.546674e-16 1.425382e-12 6.159546e-13
## GO:0097193 319/18888 1.209443e-14 1.895801e-11 8.192382e-12
## GO:0010332 52/18888 2.529209e-14 2.643023e-11 1.142137e-11
## GO:0051402 292/18888 8.050039e-14 6.309218e-11 2.726421e-11
## GO:0043523 244/18888 1.817492e-13 1.139567e-10 4.924446e-11
## GO:0097305 259/18888 3.899605e-13 1.757690e-10 7.595558e-11
## geneID
## GO:0009411 BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/CASP9
## GO:0097193 BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/MSH6/CASP9/ATM
## GO:0010332 BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/PRKAA1/ATM
## GO:0051402 ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/XIAP/CTNNB1/PIK3CA/CCND1/CASP9/ATM
## GO:0043523 ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PIK3CA/CCND1/CASP9/ATM
## GO:0097305 FOXO3/IGF1R/ACACA/BAK1/PARP1/CTNNB1/EIF4G1/CDKN1A/TYMS/CLDN7/CTNNA1/AKT1/PRKAA1
## Count
## GO:0009411 13
## GO:0097193 15
## GO:0010332 9
## GO:0051402 14
## GO:0043523 13
## GO:0097305 13
## ID Description
## GO:0017053 GO:0017053 transcription repressor complex
## GO:0097136 GO:0097136 Bcl-2 family protein complex
## GO:0005901 GO:0005901 caveola
## GO:0038143 GO:0038143 ERBB3:ERBB2 complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0044853 GO:0044853 plasma membrane raft
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0017053 5/55 77/19894 2.277285e-06 0.0002261493 0.0001179340
## GO:0097136 3/55 10/19894 2.366726e-06 0.0002261493 0.0001179340
## GO:0005901 5/55 82/19894 3.112146e-06 0.0002261493 0.0001179340
## GO:0038143 2/55 2/19894 7.504712e-06 0.0003874416 0.0002020458
## GO:0090571 3/55 15/19894 8.886276e-06 0.0003874416 0.0002020458
## GO:0044853 5/55 113/19894 1.500382e-05 0.0005451389 0.0002842830
## geneID Count
## GO:0017053 FOXO3/MYC/TP53/CTNNB1/CCND1 5
## GO:0097136 BCL2/BAK1/BCL2L11 3
## GO:0005901 IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1 5
## GO:0038143 ERBB3/ERBB2 2
## GO:0090571 FOXO3/MYC/CTNNB1 3
## GO:0044853 IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1 5
## ID Description GeneRatio
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 2/4
## GO:0004860 GO:0004860 protein kinase inhibitor activity 2/4
## GO:0019210 GO:0019210 kinase inhibitor activity 2/4
## GO:0051219 GO:0051219 phosphoprotein binding 2/4
## GO:0019887 GO:0019887 protein kinase regulator activity 2/4
## GO:0099104 GO:0099104 potassium channel activator activity 1/4
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0045309 59/18522 5.960670e-05 0.001149206 0.0001466291 MAPK3/YWHAB 2
## GO:0004860 73/18522 9.146013e-05 0.001149206 0.0001466291 AKT1/YWHAB 2
## GO:0019210 78/18522 1.044732e-04 0.001149206 0.0001466291 AKT1/YWHAB 2
## GO:0051219 93/18522 1.486690e-04 0.001226519 0.0001564936 MAPK3/YWHAB 2
## GO:0019887 232/18522 9.218946e-04 0.004986238 0.0006362027 AKT1/YWHAB 2
## GO:0099104 5/18522 1.079447e-03 0.004986238 0.0006362027 AKT1 1
## ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0071276 GO:0071276
## GO:0070302 GO:0070302
## GO:0014044 GO:0014044
## GO:0070849 GO:0070849
## Description
## GO:0051054 positive regulation of DNA metabolic process
## GO:0032872 regulation of stress-activated MAPK cascade
## GO:0071276 cellular response to cadmium ion
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0014044 Schwann cell development
## GO:0070849 response to epidermal growth factor
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051054 3/4 301/18888 1.584016e-05 0.003498466 0.0008218221
## GO:0032872 2/4 35/18888 1.996811e-05 0.003498466 0.0008218221
## GO:0071276 2/4 37/18888 2.234770e-05 0.003498466 0.0008218221
## GO:0070302 2/4 38/18888 2.358757e-05 0.003498466 0.0008218221
## GO:0014044 2/4 42/18888 2.888073e-05 0.003498466 0.0008218221
## GO:0070849 2/4 46/18888 3.470744e-05 0.003498466 0.0008218221
## geneID Count
## GO:0051054 AKT1/MAPK3/FOXM1 3
## GO:0032872 MAPK3/FOXM1 2
## GO:0071276 AKT1/MAPK3 2
## GO:0070302 MAPK3/FOXM1 2
## GO:0014044 AKT1/MAPK3 2
## GO:0070849 AKT1/MAPK3 2
## ID Description GeneRatio BgRatio pvalue
## GO:0098978 GO:0098978 glutamatergic synapse 2/4 409/19894 0.002461462
## GO:0005925 GO:0005925 focal adhesion 2/4 421/19894 0.002606078
## GO:0030055 GO:0030055 cell-substrate junction 2/4 431/19894 0.002729650
## GO:0031143 GO:0031143 pseudopodium 1/4 18/19894 0.003614545
## p.adjust qvalue geneID Count
## GO:0098978 0.01807272 0.00951196 AKT1/MAPK3 2
## GO:0005925 0.01807272 0.00951196 MAPK3/YWHAB 2
## GO:0030055 0.01807272 0.00951196 MAPK3/YWHAB 2
## GO:0031143 0.01807272 0.00951196 MAPK3 1
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 12/64
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 11/64
## GO:0030971 GO:0030971 receptor tyrosine kinase binding 6/64
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 3/64
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 9/64
## GO:0035173 GO:0035173 histone kinase activity 4/64
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 7.391982e-08 2.661113e-05 1.244965e-05
## GO:0004674 427/18522 2.130897e-07 3.523815e-05 1.648568e-05
## GO:0030971 81/18522 3.549755e-07 3.523815e-05 1.648568e-05
## GO:0043125 5/18522 3.915350e-07 3.523815e-05 1.648568e-05
## GO:0031625 305/18522 9.848097e-07 6.554912e-05 3.066625e-05
## GO:0035173 23/18522 1.092485e-06 6.554912e-05 3.066625e-05
## geneID
## GO:0140297 BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/PCNA/ETS1
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PRKAA1/ATM
## GO:0030971 ERBB2/TP53/IRS1/PIK3R1/PCNA/SQSTM1
## GO:0043125 ERBB3/ERBB2/PIK3R1
## GO:0031625 ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0035173 PRKCA/CHEK1/PRKAA1/ATM
## Count
## GO:0140297 12
## GO:0004674 11
## GO:0030971 6
## GO:0043125 3
## GO:0031625 9
## GO:0035173 4
## ID Description GeneRatio BgRatio
## GO:0009411 GO:0009411 response to UV 14/65 154/18888
## GO:0070482 GO:0070482 response to oxygen levels 16/65 354/18888
## GO:0010332 GO:0010332 response to gamma radiation 9/65 52/18888
## GO:0000302 GO:0000302 response to reactive oxygen species 13/65 203/18888
## GO:0097193 GO:0097193 intrinsic apoptotic signaling pathway 15/65 319/18888
## GO:0031960 GO:0031960 response to corticosteroid 12/65 156/18888
## pvalue p.adjust qvalue
## GO:0009411 1.341650e-16 4.424762e-13 2.008238e-13
## GO:0070482 4.659647e-14 7.683758e-11 3.487378e-11
## GO:0010332 1.245693e-13 9.012880e-11 4.090618e-11
## GO:0000302 1.744763e-13 9.012880e-11 4.090618e-11
## GO:0097193 1.810339e-13 9.012880e-11 4.090618e-11
## GO:0031960 1.814404e-13 9.012880e-11 4.090618e-11
## geneID
## GO:0009411 BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/CASP9/PCNA
## GO:0070482 FOXO3/BCL2/MYC/CASP3/TP53/PDK1/TFRC/CDKN1A/NDRG1/AKT1/ACVRL1/EEF2K/PRKAA1/CASP9/ATM/BIRC2
## GO:0010332 BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/PRKAA1/ATM
## GO:0000302 FOXO3/BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/AKT1/MAPK9/PRKAA1/ATM/PCNA
## GO:0097193 BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/MSH6/CASP9/ATM
## GO:0031960 FOXO3/IGF1R/BCL2/CASP3/BCL2L11/PARP1/PIK3CA/CDKN1A/TYMS/CASP9/PCNA/ANXA1
## Count
## GO:0009411 14
## GO:0070482 16
## GO:0010332 9
## GO:0000302 13
## GO:0097193 15
## GO:0031960 12
## ID
## GO:0097136 GO:0097136
## GO:0017053 GO:0017053
## GO:0061695 GO:0061695
## GO:0005901 GO:0005901
## GO:1902911 GO:1902911
## GO:0038143 GO:0038143
## Description
## GO:0097136 Bcl-2 family protein complex
## GO:0017053 transcription repressor complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005901 caveola
## GO:1902911 protein kinase complex
## GO:0038143 ERBB3:ERBB2 complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097136 3/65 10/19894 3.930082e-06 0.0003694095 0.0002054909
## GO:0017053 5/65 77/19894 5.246600e-06 0.0003694095 0.0002054909
## GO:0061695 8/65 308/19894 7.072064e-06 0.0003694095 0.0002054909
## GO:0005901 5/65 82/19894 7.155088e-06 0.0003694095 0.0002054909
## GO:1902911 6/65 150/19894 9.515754e-06 0.0003694095 0.0002054909
## GO:0038143 2/65 2/19894 1.051165e-05 0.0003694095 0.0002054909
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11 3
## GO:0017053 FOXO3/MYC/TP53/CTNNB1/CCND1 5
## GO:0061695 IGF1R/PIK3CA/CCND1/CDKN1A/IRS1/PIK3R1/PRKAA1/PCNA 8
## GO:0005901 IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1 5
## GO:1902911 IGF1R/CCND1/CDKN1A/IRS1/PRKAA1/PCNA 6
## GO:0038143 ERBB3/ERBB2 2
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 14/68
## GO:0051400 GO:0051400 BH domain binding 4/68
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 10/68
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 10/68
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 11/68
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 3/68
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 1.657329e-09 6.016105e-07 2.704063e-07
## GO:0051400 9/18522 2.064379e-08 3.746848e-06 1.684099e-06
## GO:0031625 305/18522 1.581950e-07 1.914159e-05 8.603587e-06
## GO:0044389 324/18522 2.765490e-07 2.509682e-05 1.128029e-05
## GO:0004674 427/18522 4.044292e-07 2.650277e-05 1.191222e-05
## GO:0043125 5/18522 4.708093e-07 2.650277e-05 1.191222e-05
## geneID
## GO:0140297 RB1/BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/AR/PCNA/ETS1
## GO:0051400 BCL2/BAK1/BCL2L1/BAX
## GO:0031625 RB1/ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0044389 RB1/ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PRKAA1/ATM
## GO:0043125 ERBB3/ERBB2/PIK3R1
## Count
## GO:0140297 14
## GO:0051400 4
## GO:0031625 10
## GO:0044389 10
## GO:0004674 11
## GO:0043125 3
## ID Description GeneRatio
## GO:0009411 GO:0009411 response to UV 15/69
## GO:0010332 GO:0010332 response to gamma radiation 11/69
## GO:0051402 GO:0051402 neuron apoptotic process 17/69
## GO:0097193 GO:0097193 intrinsic apoptotic signaling pathway 17/69
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 17/69
## GO:0104004 GO:0104004 cellular response to environmental stimulus 17/69
## BgRatio pvalue p.adjust qvalue
## GO:0009411 154/18888 9.067192e-18 3.095539e-14 1.346717e-14
## GO:0010332 52/18888 3.598885e-17 6.143296e-14 2.672645e-14
## GO:0051402 292/18888 2.991223e-16 3.404012e-13 1.480918e-13
## GO:0097193 319/18888 1.305023e-15 1.113837e-12 4.845756e-13
## GO:0071214 334/18888 2.794318e-15 1.589967e-12 6.917162e-13
## GO:0104004 334/18888 2.794318e-15 1.589967e-12 6.917162e-13
## geneID
## GO:0009411 BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/BAX/CASP9/PCNA
## GO:0010332 BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/BCL2L1/PRKAA1/BAX/ATM
## GO:0051402 RB1/ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/XIAP/CTNNB1/PIK3CA/CCND1/BCL2L1/BAX/CASP9/ATM
## GO:0097193 BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/BCL2L1/MSH6/BAX/CASP9/ATM
## GO:0071214 IGF1R/BAK1/MYC/CASP3/TP53/YAP1/PARP1/PIK3CA/MAPK3/CDKN1A/CHEK1/PIK3R1/BCL2L1/BAX/CASP9/ATM/PCNA
## GO:0104004 IGF1R/BAK1/MYC/CASP3/TP53/YAP1/PARP1/PIK3CA/MAPK3/CDKN1A/CHEK1/PIK3R1/BCL2L1/BAX/CASP9/ATM/PCNA
## Count
## GO:0009411 15
## GO:0010332 11
## GO:0051402 17
## GO:0097193 17
## GO:0071214 17
## GO:0104004 17
## ID
## GO:0097136 GO:0097136
## GO:1902911 GO:1902911
## GO:0005741 GO:0005741
## GO:0061695 GO:0061695
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## Description
## GO:0097136 Bcl-2 family protein complex
## GO:1902911 protein kinase complex
## GO:0005741 mitochondrial outer membrane
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0031968 organelle outer membrane
## GO:0019867 outer membrane
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0097136 5/69 10/19894 1.076634e-10 2.820781e-08 1.631950e-08
## GO:1902911 7/69 150/19894 8.783710e-07 7.475206e-05 4.324747e-05
## GO:0005741 8/69 219/19894 8.913377e-07 7.475206e-05 4.324747e-05
## GO:0061695 9/69 308/19894 1.141253e-06 7.475206e-05 4.324747e-05
## GO:0031968 8/69 248/19894 2.260908e-06 1.048005e-04 6.063188e-05
## GO:0019867 8/69 250/19894 2.400012e-06 1.048005e-04 6.063188e-05
## geneID Count
## GO:0097136 BCL2/BAK1/BCL2L11/BCL2L1/BAX 5
## GO:1902911 RB1/IGF1R/CCND1/CDKN1A/IRS1/PRKAA1/PCNA 7
## GO:0005741 FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR 8
## GO:0061695 RB1/IGF1R/PIK3CA/CCND1/CDKN1A/IRS1/PIK3R1/PRKAA1/PCNA 9
## GO:0031968 FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR 8
## GO:0019867 FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR 8barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_glmnet.rds")